The anaerobic digestion of Scenedesmus residues generated after a process of amino acid extraction with an extraction efficiency of 59% was thoroughly studied in 3 L working volume semi-continuous reactors. Anaerobic digestion of high concentrated Scenedesmus residues (17.6%TS) was inhibited due to ammonia and volatile acids accumulation. Dilution of the substrate to 10.5%TS avoided the inhibition of the process. The acclimation of microorganisms to the digestion of the substrate caused a further improvement in the process performance. High biogas and methane yields (409.3 and 291.5 L kg VS-1, respectively) were achieved at an organic loading rate of 3.85 g VS L-1 d(-1) with an hydraulic retention time of 20 days. Electrical and thermal energy (0.525 kWh and 2305.9 kJ per kg(dry)(-1) (cultivated biomass)) generated by the combustion of methane could be used for the different steps within the culturing of microalgae and the amino acid extraction processes. Moreover, a mass balance suggested that nitrogen and carbon dioxide needs for growing microalgae could be cut to a maximum of 30% and 25%, respectively, thanks to the coupling of anaerobic digestion to the extraction of amino acids from microalgae. (C) 2014 Elsevier B.V. All rights reserved.